HEADER REPLICATION 21-MAR-21 7M4C TITLE DNA POLYMERASE LAMBDA, TTP:AT MN2+ PRODUCT STATE TERNARY COMPLEX, 960 TITLE 2 MIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 5 KAPPA; COMPND 6 EC: 2.7.7.7,4.2.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); COMPND 11 CHAIN: T; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606 KEYWDS TIME-LAPSE CRYSTALLOGRAPHY, DOUBLE STRAND BREAK REPAIR, DNA SYNTHESIS KEYWDS 2 FIDELITY, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JAMSEN,S.H.WILSON REVDAT 2 18-OCT-23 7M4C 1 REMARK REVDAT 1 06-JUL-22 7M4C 0 JRNL AUTH J.A.JAMSEN,D.D.SHOCK,S.H.WILSON JRNL TITL WATCHING RIGHT AND WRONG NUCLEOTIDE INSERTION CAPTURES JRNL TITL 2 HIDDEN POLYMERASE FIDELITY CHECKPOINTS. JRNL REF NAT COMMUN V. 13 3193 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35680862 JRNL DOI 10.1038/S41467-022-30141-W REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.15.2-3472 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 36725 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.8740 - 4.5824 1.00 2887 144 0.1951 0.2283 REMARK 3 2 4.5824 - 3.6383 1.00 2743 148 0.1553 0.1919 REMARK 3 3 3.6383 - 3.1787 1.00 2710 134 0.1738 0.1903 REMARK 3 4 3.1787 - 2.8882 1.00 2700 144 0.1852 0.2105 REMARK 3 5 2.8882 - 2.6813 1.00 2666 131 0.1861 0.2268 REMARK 3 6 2.6813 - 2.5233 1.00 2687 141 0.1745 0.2083 REMARK 3 7 2.5233 - 2.3969 1.00 2657 137 0.1743 0.2109 REMARK 3 8 2.3969 - 2.2926 1.00 2672 142 0.1766 0.2242 REMARK 3 9 2.2926 - 2.2043 1.00 2650 137 0.1837 0.2177 REMARK 3 10 2.2043 - 2.1283 1.00 2681 134 0.1929 0.2309 REMARK 3 11 2.1283 - 2.0618 1.00 2606 141 0.2061 0.2488 REMARK 3 12 2.0618 - 2.0028 1.00 2617 134 0.2104 0.2475 REMARK 3 13 2.0028 - 1.9501 0.99 2650 132 0.2291 0.2781 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 251:320 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.407 -29.418 25.313 REMARK 3 T TENSOR REMARK 3 T11: 0.5423 T22: 0.7294 REMARK 3 T33: 0.6180 T12: 0.1609 REMARK 3 T13: -0.1501 T23: 0.0909 REMARK 3 L TENSOR REMARK 3 L11: 0.3181 L22: 0.3465 REMARK 3 L33: 0.3416 L12: -0.1475 REMARK 3 L13: -0.2744 L23: -0.0122 REMARK 3 S TENSOR REMARK 3 S11: -0.1085 S12: -0.5249 S13: 0.0851 REMARK 3 S21: 0.4359 S22: 0.0930 S23: -0.6547 REMARK 3 S31: 0.4143 S32: 0.6543 S33: 0.0007 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 321:533 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.364 -6.721 9.263 REMARK 3 T TENSOR REMARK 3 T11: 0.2425 T22: 0.2361 REMARK 3 T33: 0.2752 T12: 0.0220 REMARK 3 T13: -0.0247 T23: -0.0380 REMARK 3 L TENSOR REMARK 3 L11: 2.2124 L22: 1.3422 REMARK 3 L33: 1.6509 L12: -0.0063 REMARK 3 L13: -0.8348 L23: 0.4314 REMARK 3 S TENSOR REMARK 3 S11: 0.0925 S12: -0.1338 S13: 0.2491 REMARK 3 S21: 0.0632 S22: 0.0261 S23: -0.0852 REMARK 3 S31: -0.1438 S32: 0.0432 S33: 0.0453 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 534:575 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.942 -4.901 31.142 REMARK 3 T TENSOR REMARK 3 T11: 0.5124 T22: 0.6973 REMARK 3 T33: 0.3857 T12: -0.0170 REMARK 3 T13: -0.0152 T23: -0.1544 REMARK 3 L TENSOR REMARK 3 L11: 3.0834 L22: 1.6204 REMARK 3 L33: 0.5561 L12: -0.8963 REMARK 3 L13: 0.5536 L23: 0.2660 REMARK 3 S TENSOR REMARK 3 S11: 0.1937 S12: -0.7856 S13: -0.2556 REMARK 3 S21: 0.5442 S22: 0.0180 S23: 0.0881 REMARK 3 S31: 0.0446 S32: 0.2593 S33: 0.1609 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN T AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.912 -26.156 26.755 REMARK 3 T TENSOR REMARK 3 T11: 0.5074 T22: 0.5295 REMARK 3 T33: 0.3680 T12: 0.0047 REMARK 3 T13: 0.0400 T23: 0.1872 REMARK 3 L TENSOR REMARK 3 L11: 0.0169 L22: 0.0745 REMARK 3 L33: 0.0098 L12: 0.0102 REMARK 3 L13: 0.0097 L23: 0.0231 REMARK 3 S TENSOR REMARK 3 S11: -0.0212 S12: -0.2120 S13: 0.0716 REMARK 3 S21: -0.0531 S22: 0.1280 S23: 0.3491 REMARK 3 S31: -0.0045 S32: -0.3463 S33: -0.0022 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN T AND RESID 5:11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.654 -8.994 9.756 REMARK 3 T TENSOR REMARK 3 T11: 0.2887 T22: 0.2332 REMARK 3 T33: 0.2785 T12: 0.0117 REMARK 3 T13: -0.0255 T23: -0.0397 REMARK 3 L TENSOR REMARK 3 L11: 0.0361 L22: 0.1959 REMARK 3 L33: 0.0579 L12: 0.0726 REMARK 3 L13: 0.0160 L23: 0.0899 REMARK 3 S TENSOR REMARK 3 S11: 0.2110 S12: -0.1869 S13: -0.0300 REMARK 3 S21: 0.1007 S22: -0.0322 S23: 0.1844 REMARK 3 S31: 0.0490 S32: 0.1007 S33: 0.0006 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN P AND RESID 1:7 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.344 -14.162 9.748 REMARK 3 T TENSOR REMARK 3 T11: 0.2552 T22: 0.2550 REMARK 3 T33: 0.2186 T12: 0.0003 REMARK 3 T13: -0.0115 T23: -0.0396 REMARK 3 L TENSOR REMARK 3 L11: 0.0568 L22: 0.1135 REMARK 3 L33: 0.0581 L12: -0.0596 REMARK 3 L13: 0.0055 L23: 0.0477 REMARK 3 S TENSOR REMARK 3 S11: 0.1564 S12: -0.1281 S13: -0.0545 REMARK 3 S21: 0.0155 S22: -0.1006 S23: -0.1986 REMARK 3 S31: -0.1756 S32: -0.2403 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN D AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.384 -28.683 29.448 REMARK 3 T TENSOR REMARK 3 T11: 0.6719 T22: 0.5585 REMARK 3 T33: 0.3761 T12: -0.0015 REMARK 3 T13: 0.0564 T23: 0.0958 REMARK 3 L TENSOR REMARK 3 L11: 0.2824 L22: 0.6748 REMARK 3 L33: 1.2075 L12: 0.2377 REMARK 3 L13: 0.3155 L23: 0.9003 REMARK 3 S TENSOR REMARK 3 S11: 0.4471 S12: -0.3936 S13: -0.1912 REMARK 3 S21: 0.5628 S22: 0.1493 S23: -0.0559 REMARK 3 S31: 0.2164 S32: 0.2297 S33: 0.0927 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7M4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1001310097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36795 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.96700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 3UPQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80-95MM BICINE PH 8.3, 0.3M NA-K REMARK 280 TARTRATE, 18-22.5% POLYPURE PEG, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 28.01050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.32050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.01050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.32050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 ALA A 249 REMARK 465 THR A 250 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 252 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 ILE A 256 CG1 CG2 CD1 REMARK 470 GLU A 258 CD OE1 OE2 REMARK 470 LYS A 259 CD CE NZ REMARK 470 GLU A 261 CD OE1 OE2 REMARK 470 LYS A 265 CD CE NZ REMARK 470 LYS A 273 CE NZ REMARK 470 LEU A 286 CD1 CD2 REMARK 470 LYS A 287 CE NZ REMARK 470 PHE A 289 CE1 CE2 CZ REMARK 470 LYS A 291 CE NZ REMARK 470 VAL A 293 CG1 CG2 REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 SER A 301 OG REMARK 470 ILE A 302 CD1 REMARK 470 ILE A 305 CD1 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ARG A 308 CZ NH1 NH2 REMARK 470 ILE A 314 CD1 REMARK 470 ILE A 316 CD1 REMARK 470 LEU A 317 CD1 CD2 REMARK 470 GLU A 318 CD OE1 OE2 REMARK 470 LEU A 322 CD1 CD2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 324 CD CE NZ REMARK 470 GLU A 385 CD OE1 OE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 PHE A 406 CE2 CZ REMARK 470 LEU A 411 CD1 CD2 REMARK 470 LYS A 422 CD CE NZ REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 443 CD1 REMARK 470 ARG A 446 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 449 OD1 OD2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 LYS A 463 NZ REMARK 470 GLU A 470 CD OE1 OE2 REMARK 470 THR A 540 OG1 CG2 REMARK 470 HIS A 541 CE1 NE2 REMARK 470 LYS A 544 CG CD CE NZ REMARK 470 VAL A 545 CG1 CG2 REMARK 470 LYS A 557 CD CE NZ REMARK 470 GLU A 569 CD OE1 OE2 REMARK 470 GLU A 572 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG T 2 O3' DG T 2 C3' -0.044 REMARK 500 DA P 2 O3' DA P 2 C3' -0.038 REMARK 500 DG D 1 P DG D 1 OP3 -0.126 REMARK 500 DC D 3 O3' DC D 3 C3' -0.038 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 309 CG - SD - CE ANGL. DEV. = 10.5 DEGREES REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG P 3 OP1 - P - OP2 ANGL. DEV. = 9.0 DEGREES REMARK 500 DT P 7 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 253 45.40 -140.14 REMARK 500 CYS A 415 -137.22 -106.83 REMARK 500 ARG A 438 -53.28 -138.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 EDO A 611 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 606 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 302 O 89.6 REMARK 620 3 ILE A 305 O 81.4 75.5 REMARK 620 4 DC D 3 OP1 170.2 82.5 91.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 605 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 98.7 REMARK 620 3 ALA A 344 O 89.9 85.0 REMARK 620 4 HOH A 807 O 90.5 98.1 176.8 REMARK 620 5 DA P 5 OP1 163.1 97.9 94.6 84.1 REMARK 620 6 HOH P 209 O 72.9 169.3 88.3 88.8 91.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 604 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 382 OD2 REMARK 620 2 HIS A 486 ND1 102.0 REMARK 620 3 HOH A 757 O 73.7 86.1 REMARK 620 4 HOH A 770 O 128.7 89.9 157.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 427 OD1 2.6 REMARK 620 3 ASP A 429 OD2 94.9 96.8 REMARK 620 4 PPV A 601 O21 163.3 163.7 93.6 REMARK 620 5 PPV A 601 O22 87.0 85.4 170.3 82.3 REMARK 620 6 PPV A 601 O32 93.5 94.7 105.3 70.4 65.1 REMARK 620 7 DT P 7 OP1 92.8 90.9 94.8 100.8 94.6 158.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 603 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD1 97.1 REMARK 620 3 ASP A 490 OD2 110.4 101.3 REMARK 620 4 HOH A 785 O 77.3 164.1 94.6 REMARK 620 5 HOH A 816 O 31.0 90.8 82.1 91.7 REMARK 620 6 DT P 7 OP1 115.4 85.8 132.3 83.3 145.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 607 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 827 O REMARK 620 2 HOH A 836 O 144.7 REMARK 620 N 1 DBREF 7M4C A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 7M4C T 1 11 PDB 7M4C 7M4C 1 11 DBREF 7M4C P 1 7 PDB 7M4C 7M4C 1 7 DBREF 7M4C D 1 4 PDB 7M4C 7M4C 1 4 SEQADV 7M4C LYS A 463 UNP Q9UGP5 SER 463 CONFLICT SEQADV 7M4C GLY A 464 UNP Q9UGP5 GLN 464 CONFLICT SEQADV 7M4C A UNP Q9UGP5 GLU 466 DELETION SEQADV 7M4C A UNP Q9UGP5 ASN 467 DELETION SEQADV 7M4C A UNP Q9UGP5 GLY 468 DELETION SEQADV 7M4C A UNP Q9UGP5 GLN 469 DELETION SEQADV 7M4C A UNP Q9UGP5 GLN 470 DELETION SEQADV 7M4C THR A 471 UNP Q9UGP5 GLN 471 CONFLICT SEQADV 7M4C ALA A 543 UNP Q9UGP5 CYS 543 ENGINEERED MUTATION SEQRES 1 A 329 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU SEQRES 2 A 329 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SEQRES 3 A 329 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA SEQRES 4 A 329 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL SEQRES 5 A 329 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY SEQRES 6 A 329 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER SEQRES 7 A 329 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL SEQRES 8 A 329 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY SEQRES 9 A 329 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SEQRES 10 A 329 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR SEQRES 11 A 329 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU SEQRES 12 A 329 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN SEQRES 13 A 329 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU SEQRES 14 A 329 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA SEQRES 15 A 329 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP SEQRES 16 A 329 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SEQRES 17 A 329 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SEQRES 18 A 329 LYS GLY GLU THR LYS TYR LEU GLY VAL CYS ARG LEU PRO SEQRES 19 A 329 GLY PRO GLY ARG ARG HIS ARG ARG LEU ASP ILE ILE VAL SEQRES 20 A 329 VAL PRO TYR SER GLU PHE ALA CYS ALA LEU LEU TYR PHE SEQRES 21 A 329 THR GLY SER ALA HIS PHE ASN ARG SER MET ARG ALA LEU SEQRES 22 A 329 ALA LYS THR LYS GLY MET SER LEU SER GLU HIS ALA LEU SEQRES 23 A 329 SER THR ALA VAL VAL ARG ASN THR HIS GLY ALA LYS VAL SEQRES 24 A 329 GLY PRO GLY ARG VAL LEU PRO THR PRO THR GLU LYS ASP SEQRES 25 A 329 VAL PHE ARG LEU LEU GLY LEU PRO TYR ARG GLU PRO ALA SEQRES 26 A 329 GLU ARG ASP TRP SEQRES 1 T 11 DC DG DG DC DA DG DT DA DC DT DG SEQRES 1 P 7 DC DA DG DT DA DC DT SEQRES 1 D 4 DG DC DC DG HET PPV A 601 10 HET MN A 602 1 HET MN A 603 1 HET MN A 604 1 HET NA A 605 1 HET NA A 606 1 HET NA A 607 1 HET EDO A 608 4 HET EDO A 609 4 HET EDO A 610 4 HET EDO A 611 2 HET EDO P 101 4 HETNAM PPV PYROPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 PPV H4 O7 P2 FORMUL 6 MN 3(MN 2+) FORMUL 9 NA 3(NA 1+) FORMUL 12 EDO 5(C2 H6 O2) FORMUL 17 HOH *239(H2 O) HELIX 1 AA1 ASN A 253 GLN A 270 1 18 HELIX 2 AA2 ASP A 272 SER A 288 1 17 HELIX 3 AA3 SER A 295 CYS A 300 1 6 HELIX 4 AA4 GLY A 306 GLY A 320 1 15 HELIX 5 AA5 LEU A 322 ILE A 328 5 7 HELIX 6 AA6 SER A 331 ASN A 340 1 10 HELIX 7 AA7 GLY A 345 GLN A 355 1 11 HELIX 8 AA8 SER A 359 ALA A 367 1 9 HELIX 9 AA9 THR A 370 HIS A 379 1 10 HELIX 10 AB1 HIS A 379 LEU A 384 1 6 HELIX 11 AB2 ARG A 389 ASN A 407 1 19 HELIX 12 AB3 CYS A 415 ARG A 420 1 6 HELIX 13 AB4 ILE A 443 GLU A 454 1 12 HELIX 14 AB5 PRO A 495 SER A 497 5 3 HELIX 15 AB6 GLU A 498 GLY A 508 1 11 HELIX 16 AB7 SER A 509 LYS A 523 1 15 HELIX 17 AB8 THR A 555 LEU A 563 1 9 HELIX 18 AB9 GLU A 569 ASP A 574 5 6 SHEET 1 AA1 2 MET A 387 PRO A 388 0 SHEET 2 AA1 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA2 5 LEU A 411 ALA A 414 0 SHEET 2 AA2 5 VAL A 428 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 AA2 5 ARG A 487 VAL A 493 1 O ILE A 492 N ILE A 432 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N TYR A 473 O ILE A 491 SHEET 5 AA2 5 LEU A 457 LYS A 463 -1 N LEU A 461 O LEU A 474 SHEET 1 AA3 3 MET A 525 LEU A 527 0 SHEET 2 AA3 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 AA3 3 ARG A 549 LEU A 551 -1 O LEU A 551 N LEU A 532 SHEET 1 AA4 2 VAL A 537 ARG A 538 0 SHEET 2 AA4 2 LYS A 544 GLY A 546 -1 O VAL A 545 N VAL A 537 LINK O CYS A 300 NA NA A 606 1555 1555 2.82 LINK O ILE A 302 NA NA A 606 1555 1555 2.67 LINK O ILE A 305 NA NA A 606 1555 1555 2.76 LINK O SER A 339 NA NA A 605 1555 1555 2.38 LINK O ILE A 341 NA NA A 605 1555 1555 2.45 LINK O ALA A 344 NA NA A 605 1555 1555 2.26 LINK OD2 ASP A 382 MN MN A 604 1555 1555 2.11 LINK OD1AASP A 427 MN MN A 602 1555 1555 2.13 LINK OD1BASP A 427 MN MN A 602 1555 1555 1.85 LINK OD2AASP A 427 MN MN A 603 1555 1555 2.05 LINK OD2 ASP A 429 MN MN A 602 1555 1555 2.05 LINK OD1 ASP A 429 MN MN A 603 1555 1555 2.15 LINK ND1 HIS A 486 MN MN A 604 1555 1555 2.39 LINK OD2 ASP A 490 MN MN A 603 1555 1555 2.24 LINK O21 PPV A 601 MN MN A 602 1555 1555 2.05 LINK O22 PPV A 601 MN MN A 602 1555 1555 2.43 LINK O32 PPV A 601 MN MN A 602 1555 1555 2.15 LINK MN MN A 602 OP1 DT P 7 1555 1555 2.13 LINK MN MN A 603 O HOH A 785 1555 1555 2.44 LINK MN MN A 603 O BHOH A 816 1555 1555 2.30 LINK MN MN A 603 OP1 DT P 7 1555 1555 2.28 LINK MN MN A 604 O HOH A 757 1555 1555 2.66 LINK MN MN A 604 O HOH A 770 1555 1555 2.68 LINK NA NA A 605 O HOH A 807 1555 1555 2.50 LINK NA NA A 605 OP1 DA P 5 1555 1555 2.41 LINK NA NA A 605 O HOH P 209 1555 1555 2.62 LINK NA NA A 606 OP1 DC D 3 1555 1555 3.14 LINK NA NA A 607 O HOH A 827 1555 1555 2.87 LINK NA NA A 607 O HOH A 836 1555 1555 2.42 CISPEP 1 GLY A 508 SER A 509 0 1.89 CRYST1 56.021 62.641 140.120 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017850 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007137 0.00000